Grand Fir / Snowbrush Microbiome

2024-04-30

Preliminary data exploration

Contaminant ASVs were identified with the prevalence method using the decontam package.

Plant measures overview

Scaled-centered plant ‘health’ measures, broken down by treatment factors.

Figure 1

Model output

Formula: value ~ drought * host * site + (1|block))

Table 1
effect term estimate std.error statistic df p.value
fixed (Intercept) 0.152 0.270 0.563 19.346 0.580
fixed droughtND -0.119 0.266 -0.449 458.953 0.654
fixed hostCeanothus velutinus -0.619 0.266 -2.329 458.953 0.020
fixed inoculum_site2 0.274 0.266 1.029 458.953 0.304
fixed inoculum_site3 -0.677 0.266 -2.547 458.953 0.011
fixed inoculum_site4 0.370 0.266 1.394 458.953 0.164
fixed inoculum_site5 0.485 0.266 1.826 458.953 0.069
fixed inoculum_site6 0.259 0.266 0.974 458.953 0.331
fixed inoculum_siteSterile -0.435 0.266 -1.636 458.953 0.103
fixed droughtND:hostCeanothus velutinus 0.758 0.382 1.986 458.980 0.048
fixed droughtND:inoculum_site2 -0.171 0.376 -0.455 458.953 0.650
fixed droughtND:inoculum_site3 -0.124 0.381 -0.325 464.972 0.745
fixed droughtND:inoculum_site4 0.861 0.376 2.290 458.953 0.022
fixed droughtND:inoculum_site5 -0.209 0.376 -0.556 458.953 0.578
fixed droughtND:inoculum_site6 0.004 0.376 0.010 458.953 0.992
fixed droughtND:inoculum_siteSterile 0.374 0.376 0.994 458.953 0.321
fixed hostCeanothus velutinus:inoculum_site2 -0.070 0.376 -0.187 458.953 0.852
fixed hostCeanothus velutinus:inoculum_site3 0.469 0.376 1.247 458.953 0.213
fixed hostCeanothus velutinus:inoculum_site4 0.063 0.386 0.164 459.021 0.870
fixed hostCeanothus velutinus:inoculum_site5 -0.005 0.376 -0.013 458.953 0.990
fixed hostCeanothus velutinus:inoculum_site6 0.004 0.386 0.010 459.009 0.992
fixed hostCeanothus velutinus:inoculum_siteSterile 0.603 0.386 1.564 459.021 0.118
fixed droughtND:hostCeanothus velutinus:inoculum_site2 0.243 0.536 0.453 458.967 0.651
fixed droughtND:hostCeanothus velutinus:inoculum_site3 -0.364 0.540 -0.675 463.713 0.500
fixed droughtND:hostCeanothus velutinus:inoculum_site4 -1.004 0.543 -1.849 459.043 0.065
fixed droughtND:hostCeanothus velutinus:inoculum_site5 0.176 0.536 0.328 458.967 0.743
fixed droughtND:hostCeanothus velutinus:inoculum_site6 -0.412 0.543 -0.760 458.986 0.448
fixed droughtND:hostCeanothus velutinus:inoculum_siteSterile -0.592 0.543 -1.090 459.043 0.276



Inoculum communities overview

Taxonomic overview

Bacteria

Figure 2

Alpha diversity

Effect of Shannon diversity on plant measures

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x556928702540>

Table 2

effect group term estimate std.error statistic df p.value
fixed NA (Intercept) -1.226 0.507 -2.417 122.238 0.017
fixed NA Shannon 0.301 0.101 2.993 609.763 0.003
fixed NA hostCeanothus velutinus 0.984 2.559 0.385 610.106 0.701
fixed NA droughtND -0.187 2.351 -0.079 609.423 0.937
fixed NA inoculum_site2 1.378 1.915 0.720 609.868 0.472
fixed NA inoculum_site3 1.749 4.502 0.389 610.099 0.698
fixed NA inoculum_site4 1.827 1.868 0.978 610.007 0.328
fixed NA inoculum_site5 6.697 3.448 1.942 609.951 0.053
fixed NA inoculum_site6 6.414 1.849 3.470 610.406 0.001
fixed NA inoculum_siteSterile 7.260 2.633 2.757 609.891 0.006
fixed NA Shannon:hostCeanothus velutinus -0.301 0.424 -0.709 610.132 0.478
fixed NA Shannon:droughtND -0.033 0.409 -0.080 609.263 0.936
fixed NA hostCeanothus velutinus:droughtND 17.677 8.477 2.085 611.147 0.037
fixed NA Shannon:inoculum_site2 -0.223 0.345 -0.647 609.967 0.518
fixed NA Shannon:inoculum_site3 -0.477 0.754 -0.633 610.113 0.527
fixed NA Shannon:inoculum_site4 -0.334 0.352 -0.948 610.051 0.344
fixed NA Shannon:inoculum_site5 -1.150 0.612 -1.879 609.963 0.061
fixed NA Shannon:inoculum_site6 -1.153 0.330 -3.495 610.521 0.001
fixed NA Shannon:inoculum_siteSterile -1.391 0.457 -3.045 609.950 0.002
fixed NA hostCeanothus velutinus:inoculum_site2 -1.457 3.239 -0.450 610.782 0.653
fixed NA hostCeanothus velutinus:inoculum_site3 -2.040 6.432 -0.317 611.675 0.751
fixed NA hostCeanothus velutinus:inoculum_site4 -5.726 4.534 -1.263 610.573 0.207
fixed NA hostCeanothus velutinus:inoculum_site5 -9.239 6.982 -1.323 610.067 0.186
fixed NA hostCeanothus velutinus:inoculum_site6 -16.444 7.791 -2.111 608.880 0.035
fixed NA hostCeanothus velutinus:inoculum_siteSterile -7.195 4.427 -1.625 611.688 0.105
fixed NA droughtND:inoculum_site2 -1.482 3.252 -0.456 608.582 0.649
fixed NA droughtND:inoculum_site3 1.646 5.810 0.283 615.792 0.777
fixed NA droughtND:inoculum_site4 2.497 3.822 0.653 609.716 0.514
fixed NA droughtND:inoculum_site5 -2.968 4.505 -0.659 609.380 0.510
fixed NA droughtND:inoculum_site6 -3.067 3.816 -0.804 609.535 0.422
fixed NA droughtND:inoculum_siteSterile -5.102 4.529 -1.127 608.940 0.260
fixed NA Shannon:hostCeanothus velutinus:droughtND -2.903 1.447 -2.007 611.120 0.045
fixed NA Shannon:hostCeanothus velutinus:inoculum_site2 0.265 0.551 0.481 610.838 0.631
fixed NA Shannon:hostCeanothus velutinus:inoculum_site3 0.467 1.042 0.448 611.699 0.654
fixed NA Shannon:hostCeanothus velutinus:inoculum_site4 1.033 0.764 1.352 610.587 0.177
fixed NA Shannon:hostCeanothus velutinus:inoculum_site5 1.626 1.148 1.416 610.110 0.157
fixed NA Shannon:hostCeanothus velutinus:inoculum_site6 2.803 1.253 2.237 608.849 0.026
fixed NA Shannon:hostCeanothus velutinus:inoculum_siteSterile 1.380 0.739 1.868 611.677 0.062
fixed NA Shannon:droughtND:inoculum_site2 0.315 0.576 0.546 608.588 0.585
fixed NA Shannon:droughtND:inoculum_site3 -0.280 0.990 -0.283 615.999 0.777
fixed NA Shannon:droughtND:inoculum_site4 -0.250 0.673 -0.372 609.580 0.710
fixed NA Shannon:droughtND:inoculum_site5 0.562 0.795 0.706 609.339 0.480
fixed NA Shannon:droughtND:inoculum_site6 0.615 0.686 0.897 609.495 0.370
fixed NA Shannon:droughtND:inoculum_siteSterile 1.016 0.779 1.304 608.901 0.193
fixed NA hostCeanothus velutinus:droughtND:inoculum_site2 -13.825 9.008 -1.535 610.965 0.125
fixed NA hostCeanothus velutinus:droughtND:inoculum_site3 -23.837 11.167 -2.135 614.160 0.033
fixed NA hostCeanothus velutinus:droughtND:inoculum_site4 -12.860 9.807 -1.311 610.900 0.190
fixed NA hostCeanothus velutinus:droughtND:inoculum_site5 -6.875 11.623 -0.591 609.219 0.554
fixed NA hostCeanothus velutinus:droughtND:inoculum_site6 1.508 11.603 0.130 609.041 0.897
fixed NA hostCeanothus velutinus:droughtND:inoculum_siteSterile -11.042 9.889 -1.117 610.051 0.265
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 2.325 1.546 1.503 610.908 0.133
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 4.032 1.880 2.145 614.514 0.032
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 2.020 1.678 1.204 610.839 0.229
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 1.194 1.944 0.614 609.262 0.539
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 -0.260 1.938 -0.134 609.046 0.893
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile 1.757 1.684 1.044 609.997 0.297
ran_pars block sd__(Intercept) 0.537 NA NA NA NA
ran_pars Residual sd__Observation 0.812 NA NA NA NA

Fungi

Figure 3

Alpha diversity

Effect of Shannon diversity on plant measures

Table 3 

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x556928702540>
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) 0.849 0.357 2.379 175.175 0.018
fixed NA Shannon -0.494 0.187 -2.639 781.982 0.008
fixed NA hostCeanothus velutinus -0.898 0.731 -1.228 781.153 0.220
fixed NA droughtND -0.100 0.586 -0.170 780.300 0.865
fixed NA inoculum_site2 -0.307 0.780 -0.394 780.746 0.694
fixed NA inoculum_site3 -0.923 0.625 -1.478 782.135 0.140
fixed NA inoculum_site4 -0.526 0.439 -1.199 778.320 0.231
fixed NA inoculum_site5 -0.416 0.899 -0.463 779.825 0.644
fixed NA inoculum_site6 1.264 0.950 1.330 781.558 0.184
fixed NA inoculum_siteSterile -0.601 0.835 -0.720 779.664 0.472
fixed NA Shannon:hostCeanothus velutinus 0.253 0.368 0.686 781.374 0.493
fixed NA Shannon:droughtND 0.071 0.391 0.182 780.743 0.856
fixed NA hostCeanothus velutinus:droughtND 0.423 1.009 0.419 779.046 0.676
fixed NA Shannon:inoculum_site2 0.464 0.412 1.127 780.882 0.260
fixed NA Shannon:inoculum_site3 0.286 0.407 0.703 782.551 0.482
fixed NA Shannon:inoculum_site4 0.472 0.272 1.733 778.563 0.084
fixed NA Shannon:inoculum_site5 0.561 0.521 1.077 779.847 0.282
fixed NA Shannon:inoculum_site6 -0.426 0.463 -0.921 781.844 0.357
fixed NA Shannon:inoculum_siteSterile 0.148 0.573 0.259 779.993 0.796
fixed NA hostCeanothus velutinus:inoculum_site2 -1.597 1.728 -0.924 783.189 0.356
fixed NA hostCeanothus velutinus:inoculum_site3 1.317 1.087 1.212 779.267 0.226
fixed NA hostCeanothus velutinus:inoculum_site4 1.081 1.230 0.879 780.948 0.379
fixed NA hostCeanothus velutinus:inoculum_site5 0.875 1.388 0.630 778.872 0.529
fixed NA hostCeanothus velutinus:inoculum_site6 -1.300 1.398 -0.930 779.092 0.353
fixed NA hostCeanothus velutinus:inoculum_siteSterile 3.604 2.018 1.786 782.650 0.074
fixed NA droughtND:inoculum_site2 -0.134 1.054 -0.128 778.928 0.899
fixed NA droughtND:inoculum_site3 -0.704 0.936 -0.752 783.662 0.452
fixed NA droughtND:inoculum_site4 0.278 0.730 0.381 779.650 0.703
fixed NA droughtND:inoculum_site5 1.726 1.308 1.320 779.211 0.187
fixed NA droughtND:inoculum_site6 -1.982 1.176 -1.686 781.343 0.092
fixed NA droughtND:inoculum_siteSterile -0.932 1.574 -0.592 779.049 0.554
fixed NA Shannon:hostCeanothus velutinus:droughtND 0.107 0.564 0.189 779.603 0.850
fixed NA Shannon:hostCeanothus velutinus:inoculum_site2 0.401 0.759 0.529 783.178 0.597
fixed NA Shannon:hostCeanothus velutinus:inoculum_site3 -0.635 0.624 -1.017 779.000 0.309
fixed NA Shannon:hostCeanothus velutinus:inoculum_site4 -0.621 0.606 -1.025 781.143 0.306
fixed NA Shannon:hostCeanothus velutinus:inoculum_site5 -0.621 0.703 -0.883 779.016 0.377
fixed NA Shannon:hostCeanothus velutinus:inoculum_site6 0.524 0.674 0.778 779.068 0.437
fixed NA Shannon:hostCeanothus velutinus:inoculum_siteSterile -2.208 1.304 -1.693 782.565 0.091
fixed NA Shannon:droughtND:inoculum_site2 0.018 0.642 0.028 779.055 0.978
fixed NA Shannon:droughtND:inoculum_site3 0.468 0.656 0.713 761.413 0.476
fixed NA Shannon:droughtND:inoculum_site4 0.336 0.516 0.651 780.553 0.515
fixed NA Shannon:droughtND:inoculum_site5 -1.160 0.814 -1.425 779.215 0.155
fixed NA Shannon:droughtND:inoculum_site6 1.144 0.662 1.729 781.593 0.084
fixed NA Shannon:droughtND:inoculum_siteSterile 1.043 1.199 0.870 779.158 0.384
fixed NA hostCeanothus velutinus:droughtND:inoculum_site2 3.098 2.246 1.379 783.493 0.168
fixed NA hostCeanothus velutinus:droughtND:inoculum_site3 0.031 1.488 0.021 782.971 0.984
fixed NA hostCeanothus velutinus:droughtND:inoculum_site4 -0.831 1.480 -0.561 780.610 0.575
fixed NA hostCeanothus velutinus:droughtND:inoculum_site5 -2.121 1.903 -1.114 781.010 0.265
fixed NA hostCeanothus velutinus:droughtND:inoculum_site6 1.765 1.935 0.912 779.142 0.362
fixed NA hostCeanothus velutinus:droughtND:inoculum_siteSterile -2.625 2.547 -1.031 780.772 0.303
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site2 -1.282 1.099 -1.166 783.243 0.244
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site3 -0.417 1.000 -0.417 782.862 0.677
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site4 -0.040 0.805 -0.050 781.159 0.960
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site5 1.334 1.075 1.240 781.134 0.215
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_site6 -1.164 1.046 -1.113 778.965 0.266
fixed NA Shannon:hostCeanothus velutinus:droughtND:inoculum_siteSterile 1.589 1.822 0.872 780.899 0.384
ran_pars block sd__(Intercept) 0.339 NA NA NA NA
ran_pars Residual sd__Observation 0.879 NA NA NA NA

AMF

Figure 4

Alpha diversity

Effect of Shannon diversity on plant measures

Table 4 

## overall_transformed_plant_value ~ Shannon * host * drought * 
##     inoculum_site + (1 | block)
## <environment: 0x556928702540>
effect group term estimate std.error statistic df p.value
fixed NA (Intercept) -0.774 0.228 -3.399 342 0.001
fixed NA Shannon 0.234 0.159 1.469 342 0.143
fixed NA droughtND 0.975 0.351 2.778 342 0.006
fixed NA inoculum_site1 0.079 0.438 0.182 342 0.856
fixed NA inoculum_site2 1.292 0.612 2.111 342 0.036
fixed NA inoculum_site3 0.070 0.467 0.150 342 0.881
fixed NA inoculum_site4 0.465 0.334 1.389 342 0.166
fixed NA inoculum_site5 0.680 0.588 1.157 342 0.248
fixed NA inoculum_site6 0.413 0.535 0.773 342 0.440
fixed NA Shannon:droughtND -0.151 0.222 -0.677 342 0.499
fixed NA Shannon:inoculum_site1 -0.150 0.271 -0.552 342 0.581
fixed NA Shannon:inoculum_site2 -0.579 0.297 -1.945 342 0.053
fixed NA Shannon:inoculum_site3 -0.152 0.259 -0.586 342 0.558
fixed NA Shannon:inoculum_site4 -0.238 0.227 -1.045 342 0.297
fixed NA Shannon:inoculum_site5 -0.321 0.328 -0.976 342 0.330
fixed NA Shannon:inoculum_site6 -0.258 0.295 -0.876 342 0.382
fixed NA droughtND:inoculum_site1 0.288 0.651 0.443 342 0.658
fixed NA droughtND:inoculum_site2 -1.133 1.025 -1.105 342 0.270
fixed NA droughtND:inoculum_site3 -0.941 0.592 -1.588 342 0.113
fixed NA droughtND:inoculum_site4 -0.362 0.581 -0.623 342 0.534
fixed NA droughtND:inoculum_site5 1.175 1.236 0.951 342 0.342
fixed NA droughtND:inoculum_site6 -0.880 0.740 -1.190 342 0.235
fixed NA Shannon:droughtND:inoculum_site1 0.013 0.358 0.035 342 0.972
fixed NA Shannon:droughtND:inoculum_site2 0.577 0.445 1.298 342 0.195
fixed NA Shannon:droughtND:inoculum_site3 0.346 0.335 1.030 342 0.304
fixed NA Shannon:droughtND:inoculum_site4 0.290 0.334 0.867 342 0.386
fixed NA Shannon:droughtND:inoculum_site5 -0.365 0.555 -0.658 342 0.511
fixed NA Shannon:droughtND:inoculum_site6 0.506 0.389 1.302 342 0.194
ran_pars block sd__(Intercept) 0.000 NA NA NA NA
ran_pars Residual sd__Observation 0.912 NA NA NA NA

Comparison between inoculum and root communities

Bacteria

Figure 5

Figure 6


Not all taxa in the inoculae were subsequently found in the root samples

Figure 7


Fungi

Figure 8

Figure 9


Not all taxa in the inoculae were subsequently found in the root samples

Figure 10


AMF

Figure 11

Figure 12
Not all taxa in the inoculae were subsequently found in the root samples

Figure 13



Microbial guilds

Bacteria

I couldn’t get a trustworthy annotation of “mutualists” for bacteria, but here are probable pathogens:

Figure 14

Table 5

## value ~ proportion_pathogen * drought + (1 | block)
## <environment: 0x55692d5791c0>
effect term estimate std.error statistic df p.value species
fixed (Intercept) -0.4579 0.2353 -1.9458 27.6894 0.0619 Ceanothus
fixed proportion_pathogen 0.1621 0.5053 0.3209 480.8904 0.7484 Ceanothus
fixed droughtND 1.5430 0.2479 6.2243 477.2195 0.0000 Ceanothus
fixed proportion_pathogen:droughtND -2.3112 0.6993 -3.3049 477.2112 0.0010 Ceanothus
fixed (Intercept) -0.3939 0.2931 -1.3441 25.3702 0.1908 Abies
fixed proportion_pathogen 1.0819 0.7509 1.4409 572.5931 0.1502 Abies
fixed droughtND 0.6770 0.3000 2.2564 575.5163 0.0244 Abies
fixed proportion_pathogen:droughtND -1.8231 0.9838 -1.8530 574.8925 0.0644 Abies

Fungi

How does the proportion of mutualist fungi relate to indicators of plant health?

In the following figure, the X-axis represents the proportion of fungi that could be identified to a mutualistic guild; the Y-axis represents the value of the various measures of plant success (facets). Y-axis scales vary between facets.

Figure 15

We see an opposite pattern when looking at the proportions of putatively pathogenic fungi

Figure 16

Table 6
effect term estimate std.error statistic df p.value species
fixed (Intercept) -0.3847 0.1554 -2.4763 10.3037 0.0321 Ceanothus
fixed proportion_pathogen -0.0765 0.3571 -0.2142 481.0194 0.8305 Ceanothus
fixed droughtND 0.6741 0.1251 5.3868 478.1963 0.0000 Ceanothus
fixed proportion_pathogen:droughtND 0.4320 0.4147 1.0417 479.3039 0.2981 Ceanothus
fixed (Intercept) -0.0686 0.2101 -0.3265 7.1573 0.7534 Abies
fixed proportion_pathogen -0.1818 0.2842 -0.6398 573.1129 0.5226 Abies
fixed droughtND 0.1919 0.0886 2.1646 573.6108 0.0308 Abies
fixed proportion_pathogen:droughtND -0.6103 0.4252 -1.4352 573.5293 0.1518 Abies
fixed (Intercept) -0.2647 0.1512 -1.7507 10.5999 0.1088 Ceanothus
fixed proportion_mutualist -0.3757 0.2059 -1.8246 478.0381 0.0687 Ceanothus
fixed droughtND 0.5233 0.1298 4.0310 477.7130 0.0001 Ceanothus
fixed proportion_mutualist:droughtND 0.7054 0.2734 2.5804 478.2614 0.0102 Ceanothus
fixed (Intercept) -0.1068 0.2240 -0.4767 9.3338 0.6446 Abies
fixed proportion_mutualist 0.0251 0.1663 0.1506 572.6223 0.8803 Abies
fixed droughtND 0.1075 0.1439 0.7472 573.1318 0.4553 Abies
fixed proportion_mutualist:droughtND 0.0540 0.2282 0.2368 574.9668 0.8129 Abies



Beta-Diversity

Bacteria

Figure 17

Table 7

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
host 1 3.8414120 0.0687480 12.836684 0.001
inoculum_site 5 7.1862718 0.1286094 4.802812 0.001
drought 1 0.8088162 0.0144750 2.702787 0.001
host:inoculum_site 5 3.6135887 0.0646707 2.415075 0.001
host:drought 1 0.7562988 0.0135351 2.527292 0.001
inoculum_site:drought 5 1.9283329 0.0345105 1.288766 0.005
host:inoculum_site:drought 5 1.8316856 0.0327808 1.224173 0.018
Residual 120 35.9103196 0.6426704 NA NA
Total 143 55.8767255 1.0000000 NA NA

Fungi

Figure 18

Table 7

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
host 1 1.8555637 0.0288094 5.687460 0.001
inoculum_site 5 14.1030579 0.2189636 8.645414 0.001
drought 1 0.6383236 0.0099106 1.956516 0.007
host:inoculum_site 5 4.4734164 0.0694541 2.742280 0.001
host:drought 1 0.4690934 0.0072831 1.437811 0.082
inoculum_site:drought 5 2.0071801 0.0311634 1.230436 0.052
host:inoculum_site:drought 5 1.7109789 0.0265646 1.048859 0.351
Residual 120 39.1506299 0.6078512 NA NA
Total 143 64.4082440 1.0000000 NA NA

AMF

Figure 19

Table 8

## PermANOVA run without outlier Sterile-inoculum root samples...
term df SumOfSqs R2 statistic p.value
inoculum_site 6 6.9907731 0.2129210 2.9819777 0.001
drought 1 0.3007071 0.0091588 0.7696159 0.777
inoculum_site:drought 6 2.0978089 0.0638939 0.8948394 0.770
Residual 60 23.4434120 0.7140263 NA NA
Total 73 32.8327011 1.0000000 NA NA



Important Taxa

These taxa were identified by both Random Forest models and corncob as being important predictors of the various experimental conditions & had significant differential abundance between levels of those variables

Bacteria

Differential Abundance

Figure 20

Relative Abundances of ‘important’ taxa in root samples

Figure 21

Fungi

Differential Abundance

Figure 22

No fungal taxa were found to have significant differential abundance between drought levels

Relative Abundances of ‘important’ taxa in root samples

Figure 23


AMF

Differential Abundance

Figure 24

No fungal taxa were found to have significant differential abundance between drought levels

Relative Abundances of ‘important’ taxa in root samples

Figure 25



Phylogenetic properties

Bacteria

  • Still kind of messy
  • What specific questions do we need to address with this?

Fungi

  • Phylogenetic dispersion is tricky with ITS markers :(
  • Could try GhostTree for fungi of interest that come up as ‘unknown’



Network properties

Selected network attributes

Figure 26

Network properties vs Plant Health

(Composite scaled-centered plant health measures)

Table 9

## Plant_Growth_Response ~ species * kingdom * (n_vertices + n_edges + 
##     mean_dist + mean_betweenness + mean_closeness + global_effic + 
##     clustering_coeficient + max_degree)
Table 10
term estimate std.error statistic p.value
(Intercept) -0.5543907 2.1316421 -0.2600768 0.7948531
speciesSnowbrush 0.6542343 2.0842474 0.3138947 0.7536604
kingdomBacteria 0.7978266 2.1468131 0.3716330 0.7102375
kingdomFungi -0.8562899 1.6360027 -0.5234037 0.6007986
n_vertices 0.0291094 0.0107670 2.7035694 0.0069655
n_edges -0.0024261 0.0012869 -1.8852135 0.0596639
mean_dist 0.1615886 0.4334980 0.3727550 0.7094025
mean_betweenness -0.0179824 0.0069480 -2.5881320 0.0097768
mean_closeness 3.5648124 6.0927745 0.5850885 0.5586080
global_effic 0.2433596 2.2006359 0.1105861 0.9119647
clustering_coeficient -0.0752389 0.5987383 -0.1256624 0.9000221
max_degree -0.0063211 0.0050534 -1.2508744 0.2112458
speciesSnowbrush:kingdomBacteria -2.5890158 2.2315970 -1.1601628 0.2462338
speciesSnowbrush:kingdomFungi NA NA NA NA
speciesSnowbrush:n_vertices -0.0143278 0.0070904 -2.0207346 0.0435487
speciesSnowbrush:n_edges 0.0009879 0.0005423 1.8215202 0.0687988
speciesSnowbrush:mean_dist -0.1533864 0.4203805 -0.3648752 0.7152746
speciesSnowbrush:mean_betweenness 0.0087602 0.0042885 2.0427016 0.0413195
speciesSnowbrush:mean_closeness -3.8685083 6.0811564 -0.6361468 0.5248128
speciesSnowbrush:global_effic -0.3158048 2.1737739 -0.1452795 0.8845168
speciesSnowbrush:clustering_coeficient 0.1621361 0.5926434 0.2735812 0.7844578
speciesSnowbrush:max_degree 0.0049979 0.0031582 1.5825020 0.1138219
kingdomBacteria:n_vertices -0.0329669 0.0121835 -2.7058628 0.0069179
kingdomFungi:n_vertices -0.0165321 0.0091401 -1.8087389 0.0707640
kingdomBacteria:n_edges 0.0024004 0.0030422 0.7890472 0.4302542
kingdomFungi:n_edges 0.0016689 0.0011998 1.3909118 0.1645329
kingdomBacteria:mean_dist -0.1937280 0.4375996 -0.4427060 0.6580653
kingdomFungi:mean_dist 0.1932210 0.3090319 0.6252461 0.5319390
kingdomBacteria:mean_betweenness 0.0200096 0.0073609 2.7183639 0.0066635
kingdomFungi:mean_betweenness 0.0098666 0.0061194 1.6123424 0.1071738
kingdomBacteria:mean_closeness -3.7281546 6.0969418 -0.6114795 0.5410083
kingdomFungi:mean_closeness -1.1787054 5.0414341 -0.2338036 0.8151809
kingdomBacteria:global_effic -0.5827634 2.2369624 -0.2605155 0.7945148
kingdomFungi:global_effic 1.1682005 1.7966026 0.6502276 0.5156808
kingdomBacteria:clustering_coeficient 0.4787035 0.6264813 0.7641146 0.4449625
kingdomFungi:clustering_coeficient -0.6050180 0.4565936 -1.3250690 0.1854230
kingdomBacteria:max_degree 0.0182595 0.0103733 1.7602447 0.0786437
kingdomFungi:max_degree 0.0034425 0.0043117 0.7984040 0.4248081
speciesSnowbrush:kingdomBacteria:n_vertices 0.0326440 0.0120103 2.7180067 0.0066707
speciesSnowbrush:kingdomFungi:n_vertices NA NA NA NA
speciesSnowbrush:kingdomBacteria:n_edges -0.0025587 0.0034005 -0.7524393 0.4519476
speciesSnowbrush:kingdomFungi:n_edges NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_dist 0.4770298 0.4435839 1.0753992 0.2824314
speciesSnowbrush:kingdomFungi:mean_dist NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_betweenness -0.0214609 0.0063300 -3.3903559 0.0007228
speciesSnowbrush:kingdomFungi:mean_betweenness NA NA NA NA
speciesSnowbrush:kingdomBacteria:mean_closeness 6.3019795 6.1167331 1.0302852 0.3031022
speciesSnowbrush:kingdomFungi:mean_closeness NA NA NA NA
speciesSnowbrush:kingdomBacteria:global_effic 3.5991501 2.4129321 1.4916085 0.1360880
speciesSnowbrush:kingdomFungi:global_effic NA NA NA NA
speciesSnowbrush:kingdomBacteria:clustering_coeficient -1.3580924 0.7086829 -1.9163612 0.0555776
speciesSnowbrush:kingdomFungi:clustering_coeficient NA NA NA NA
speciesSnowbrush:kingdomBacteria:max_degree -0.0102114 0.0123216 -0.8287420 0.4074299
speciesSnowbrush:kingdomFungi:max_degree NA NA NA NA


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Soil chemistry

Overview of soil properties for each inoculum source:

Testing for significant differences between the samples…

Here are the soil properties that differ significantly between inoculum sources. Sterile inoculum soils are set as the intercept. The stats below pretty nicely reflect the obvious patterns in the overall figure.
term estimate std.error statistic p.value
Mn 1.248 0.268 4.658 0.000
NH4 0.770 0.268 2.875 0.004
Fe:inoc_site1 1.516 0.328 4.618 0.000
K:inoc_site1 0.904 0.328 2.753 0.006
NO3:inoc_site1 -0.793 0.328 -2.417 0.016
TKN:inoc_site1 0.735 0.328 2.240 0.026
Zn:inoc_site1 1.160 0.328 3.536 0.000
Fe:inoc_site2 0.831 0.328 2.532 0.012
K:inoc_site2 0.801 0.328 2.440 0.015
Mn:inoc_site2 -1.081 0.328 -3.294 0.001
TKN:inoc_site2 0.660 0.328 2.010 0.045
Mn:inoc_site3 -1.526 0.328 -4.648 0.000
NH4:inoc_site3 -0.976 0.328 -2.973 0.003
Zn:inoc_site3 -0.693 0.328 -2.112 0.035
C:N:inoc_site4 -0.893 0.328 -2.721 0.007
EC:inoc_site4 -1.026 0.328 -3.127 0.002
Mn:inoc_site4 -1.349 0.328 -4.110 0.000
B:inoc_site5 1.369 0.328 4.171 0.000
Ca:inoc_site5 1.192 0.328 3.631 0.000
K:inoc_site5 0.683 0.328 2.080 0.038
Mg:inoc_site5 0.682 0.328 2.078 0.039
Mn:inoc_site5 -1.099 0.328 -3.350 0.001
NO3:inoc_site5 1.854 0.328 5.649 0.000
TKN:inoc_site5 1.022 0.328 3.114 0.002
Zn:inoc_site5 1.448 0.328 4.412 0.000
B:inoc_site6 0.918 0.328 2.798 0.005
Mn:inoc_site6 -1.535 0.328 -4.678 0.000
NH4:inoc_site6 -0.754 0.328 -2.299 0.022
NO3:inoc_site6 1.273 0.328 3.880 0.000
Zn:inoc_site6 1.290 0.328 3.932 0.000